biology/picard-tools: CLI tools for manipulating sequencing data

Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
This commit is contained in:
Jason W. Bacon 2020-06-13 13:54:47 +00:00
parent 3fadea798f
commit 4a5b8a759b
Notes: svn2git 2021-03-31 03:12:20 +00:00
svn path=/head/; revision=538672
6 changed files with 170 additions and 0 deletions

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@ -114,6 +114,7 @@
SUBDIR += phred
SUBDIR += phylip
SUBDIR += phyml
SUBDIR += picard-tools
SUBDIR += plink
SUBDIR += primer3
SUBDIR += prodigal

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# $FreeBSD$
PORTNAME= picard
DISTVERSION= 2.22.9
CATEGORIES= biology java
MASTER_SITES= http://github.com/broadinstitute/picard/releases/download/${PORTVERSION}/
PKGNAMESUFFIX= -tools
DISTNAME= ${PORTNAME}
EXTRACT_SUFX= .jar
MAINTAINER= jwb@FreeBSD.org
COMMENT= CLI tools for manipulating high-throughput sequencing (HTS) data
LICENSE= MIT
RUN_DEPENDS= samtools:biology/samtools
USE_JAVA= 1.8+
JAVA_RUN= yes
SUB_FILES= picard
NO_BUILD= yes
NO_ARCH= yes
PLIST_FILES= bin/picard ${JAVAJARDIR}/picard.jar
do-extract:
# No extract
do-install:
${INSTALL_DATA} ${DISTDIR}/${DISTNAME}${EXTRACT_SUFX} \
${STAGEDIR}${JAVAJARDIR}
${INSTALL_SCRIPT} ${WRKDIR}/picard ${STAGEDIR}${PREFIX}/bin
.include <bsd.port.mk>

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[00:00:00] Creating the reference jail... done
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[00:00:07] Starting jail 12-1-amd64-default
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[00:00:12] Deleting stale symlinks... done
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[00:00:12] Cleaning the build queue
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[00:00:12] Building 28 packages using 4 builders
[00:00:12] Starting/Cloning builders
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[00:17:20] Stopping 4 builders
[00:17:21] Error: Depends failed to build
[00:17:21] Failed ports: java/openjdk8:build
[00:17:21] Cleaning up
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TIMESTAMP = 1591387929
SHA256 (picard.jar) = a3d8830f68443a745cca9e1bab9adbc1c435fe3639709b118f5a89858a12a362
SIZE (picard.jar) = 17520128

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#!/bin/sh -e
if [ $# = 0 ] || [ $1 = -h ]; then
cat << EOM
"picard" is a wrapper script around the Picard tools Java jar.
To run Picard tools the traditional way, run
java -jar %%JAVAJARDIR%%/picard.jar [args]
EOM
fi
java -jar %%JAVAJARDIR%%/picard.jar "$@"

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Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
WWW: https://broadinstitute.github.io/picard/